Local alignment

Local alignment gives the alignment order in which only the most similar regions of n sequences are aligned in n dimensions. The measure of similarity will depend on the parameters used for registering a mismatch. The cells of scoring matrix are more homogeneous than those of global alignment matrix. No highest score less than zero is recorded and a pointer is only added when a score is greater than zero. In the end, trace-back begins from the maximum score and ends at the origin of matrix. This variation of assigning scores in a matrix makes local alignment more stringent than global alignment.